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Lalitha N, Ronald BSM, Chitra MA, Jangam AK, Katneni VK, Suganya PN, Senthilnayagam H, Senthilkumar TMA, Muralidhar M. Exploration of the candidate beneficial bacteria for Penaeus vannamei culture by core microbiome analysis using amplicon sequencing. Lett Appl Microbiol 2023; 76:ovad087. [PMID: 37541955 DOI: 10.1093/lambio/ovad087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/28/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023]
Abstract
Globally, Penaeus vannamei is the vital species in aquaculture production. Beneficial bacterial exploration of gut, sediment, and water were investigated in P. vannamei culture using Illumina Miseq sequencing of 16S RNA V3-V4 hypervariable regions. Predominant phyla identified were Proteobacteria, Tenericutes, Bacteroidetes in gut; Proteobacteria, Bacteroidetes, Planctomycetes in sediment and Cyanobacteria, Proteobacteria, and Planctomycetes in water. In total, 46 phyla, 509 families and 902 genera; 70 phyla, 735 families and 1255 genera; 55 phyla, 580 families and 996 genera were observed in gut, sediment and water, respectively. Diversity of microbial communities in respect of observed Operational Taxonomic Units, diversity indices (Shannon and Simpson), richness index (Chao1) were significantly high P (<0.05) in 60 DoC in gut and 30 DoC in sediment. Beta diversity indicated separate clusters for bacterial communities in gut, sediment and water samples and formation of distinct community profiles. Core microbiome in P. vannamei rearing ponds over a time consisted of 9, 21, and 20 OTUs in gut, rearing water and sediment, respectively. This study helps to intervene with suitable beneficial microbes to establish an aquaculture system thereby contributes to enhance the productivity, improve water quality and pond bottom condition, and control the pathogenic agents at each stage of the culture.
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Affiliation(s)
- Natarajan Lalitha
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
- Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600007, India
| | | | - Murugesan Ananda Chitra
- Centre for Animal Health Studies, Madhavaram Milk Colony, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600051, India
| | - Ashok Kumar Jangam
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
| | - Vinaya Kumar Katneni
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
| | - Panjan Nathamuni Suganya
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
| | - Hemalatha Senthilnayagam
- Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600007, India
| | | | - Moturi Muralidhar
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
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Albright S, Louca S. Trait biases in microbial reference genomes. Sci Data 2023; 10:84. [PMID: 36759614 PMCID: PMC9911409 DOI: 10.1038/s41597-023-01994-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.
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Affiliation(s)
- Sage Albright
- Department of Biology, University of Oregon, Eugene, USA
| | - Stilianos Louca
- Department of Biology, University of Oregon, Eugene, USA. .,Institute of Ecology and Evolution, University of Oregon, Eugene, USA.
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He J, Jia M, Wang J, Wu Z, Shao S, He Y, Zhang X, Buttino I, Liao Z, Yan X. Mytilus farming drives higher local bacterial diversity and facilitates the accumulation of aerobic anoxygenic photoheterotrophic related genera. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:158861. [PMID: 36419274 DOI: 10.1016/j.scitotenv.2022.158861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/02/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Research to assess the impacts of mariculture on the microbiota of the surrounding environment is still inadequate. Here, we examined the effects of Mytilus coruscus farming on the diversity of bacterial community in surrounding seawater using field investigations and indoor simulations, focusing on the variation of members of aerobic anoxygenic photoheterotrophic (AAP) bacteria. In the field, Mytilus farming shaped bacterial community and significantly increased their diversity, including biomass, OTUs, Shannon, relative abundance, number of enriched species, as compared with the non-farming area. Higher abundance of AAP related genera was observed in the Mytilus farming seawater. Under the controlled condition, the presence of M. coruscus significantly shaped the bacterial community composition and caused species composition to become similar after 10 days. Furthermore, the presence of M. coruscus consistently strengthened local diversity in seawater bacterial community, with linkages to the recruitment of AAP members as well. In addition, the tissue-related composition of M. coruscus significantly differed from those in seawater. Our findings highlight a ecological importance of Mytilus farming, as process that shape surrounding water-cultured bacterial community and offer experimental evidence for the accumulation of AAP-related genera in aquaculture systems.
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Affiliation(s)
- Jianyu He
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City 316022, Zhejiang, China
| | - Mengxue Jia
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City 316022, Zhejiang, China
| | - Jianxin Wang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Ziqi Wu
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City 316022, Zhejiang, China
| | - Shuai Shao
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City 316022, Zhejiang, China
| | - Yutang He
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City 316022, Zhejiang, China
| | - Xiaolin Zhang
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City 316022, Zhejiang, China
| | - Isabella Buttino
- Italian Institute for Environmental Protection and Research (ISPRA), Via Vitaliano Brancati 48, 00144 Rome, Italy
| | - Zhi Liao
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City 316022, Zhejiang, China
| | - Xiaojun Yan
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City 316022, Zhejiang, China.
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Da Silva RRP, White CA, Bowman JP, Ross DJ. Composition and functionality of bacterioplankton communities in marine coastal zones adjacent to finfish aquaculture. MARINE POLLUTION BULLETIN 2022; 182:113957. [PMID: 35872476 DOI: 10.1016/j.marpolbul.2022.113957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Finfish aquaculture is a fast-growing primary industry and is increasingly common in coastal ecosystems. Bacterioplankton is ubiquitous in marine environment and respond rapidly to environmental changes. Changes in bacterioplankton community are not well understood in semi-enclosed stratified embayments. This study aims to examine aquaculture effects in the composition and functional profiles of the bacterioplankton community using amplicon sequencing along a distance gradient from two finfish leases in a marine embayment. Results revealed natural stratification in bacterioplankton associated to NOx, conductivity, salinity, temperature and PO4. Among the differentially abundant bacteria in leases, we found members associated with nutrient enrichment and aquaculture activities. Abundant predicted functions near leases were assigned to organic matter degradation, fermentation, and antibiotic resistance. This study provides a first effort to describe changes in the bacterioplankton community composition and function due to finfish aquaculture in a semi-enclosed and highly stratified embayment with a significant freshwater input.
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Affiliation(s)
- R R P Da Silva
- Institute for Marine and Antarctic Studies (IMAS), Nubeena Crescent, Taroona, Tasmania 7053, Australia.
| | - C A White
- Institute for Marine and Antarctic Studies (IMAS), Nubeena Crescent, Taroona, Tasmania 7053, Australia
| | - J P Bowman
- Tasmanian Institute of Agriculture (TIA), University of Tasmania, Hobart, Tasmania 7001, Australia
| | - D J Ross
- Institute for Marine and Antarctic Studies (IMAS), Nubeena Crescent, Taroona, Tasmania 7053, Australia
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Wang H, Zhang K, Wu L, Qin Q, He Y. Prediction of Pathogenic Factors in Dysbiotic Gut Microbiomes of Colorectal Cancer Patients Using Reverse Microbiomics. Front Oncol 2022; 12:882874. [PMID: 35574378 PMCID: PMC9091335 DOI: 10.3389/fonc.2022.882874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Background Gut microbiome plays a crucial role in the formation and progression of colorectal cancer (CRC). To better identify the underlying gene-level pathogenic mechanisms of microbiome-associated CRC, we applied our newly developed Reverse Microbiomics (RM) to predict potential pathogenic factors using the data of microbiomes in CRC patients. Results Our literature search first identified 40 bacterial species enriched and 23 species depleted in the guts of CRC patients. These bacteria were systematically modeled and analyzed using the NCBI Taxonomy ontology. Ten species, including 6 enriched species (e.g., Bacteroides fragilis, Fusobacterium nucleatum and Streptococcus equinus) and 4 depleted species (e.g., Bacteroides uniformis and Streptococcus thermophilus) were chosen for follow-up comparative genomics analysis. Vaxign was used to comparatively analyze 47 genome sequences of these ten species. In total 18 autoantigens were predicted to contribute to CRC formation, six of which were reported with experimental evidence to be correlated with drug resistance and/or cell invasiveness of CRC. Interestingly, four human homology proteins (EDK89078.1, EDK87700.1, EDK89777.1, and EDK89145.1) are conserved among all enriched strains. Furthermore, we predicted 76 potential virulence factors without homology to human proteins, including two riboflavin synthase proteins, three ATP-binding cassettes (ABC) transporter protein family proteins, and 12 outer membrane proteins (OMPs). Riboflavin synthase is present in all the enriched strains but not in depleted species. The critical role of riboflavin synthase in CRC development was further identified from its hub role in our STRING-based protein-protein interaction (PPI) network analysis and from the finding of the riboflavin metabolism as the most significantly enriched pathway in our KEGG pathway analysis. A novel model of the CRC pathogenesis involving riboflavin synthase and other related proteins including TpiA and GrxC was further proposed. Conclusions The RM strategy was used to predict 18 autoantigens and 76 potential virulence factors from CRC-associated microbiome data. In addition to many of these autoantigens and virulence factors experimentally verified as reported in the literature, our study predicted many new pathogenetic factors and developed a new model of CRC pathogenesis involving the riboflavin synthase from the enriched colorectal bacteria and other associated proteins.
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Affiliation(s)
- Haihe Wang
- Department of Immunology and Pathogen Biology, Lishui University, Lishui, China
| | - Kaibo Zhang
- Department of Immunology and Pathogen Biology, Lishui University, Lishui, China
| | - Lin Wu
- Center of Computer Experiment, Lishui University, Lishui, China
| | - Qian Qin
- Department of Immunology and Pathogen Biology, Lishui University, Lishui, China
| | - Yongqun He
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, United States.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States.,Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States.,Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, United States
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Bacterial community in response to packaging conditions in farmed gilthead seabream. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2021.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Impact of Marine Aquaculture on the Microbiome Associated with Nearby Holobionts: The Case of Patella caerulea Living in Proximity of Sea Bream Aquaculture Cages. Microorganisms 2021; 9:microorganisms9020455. [PMID: 33671759 PMCID: PMC7927081 DOI: 10.3390/microorganisms9020455] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 01/04/2023] Open
Abstract
Aquaculture plays a major role in the coastal economy of the Mediterranean Sea. This raises the issue of the impact of fish cages on the surrounding environment. Here, we explore the impact of aquaculture on the composition of the digestive gland microbiome of a representative locally dwelling wild holobiont, the grazer gastropod Patella caerulea, at an aquaculture facility located in Southern Sicily, Italy. The microbiome was assessed in individuals collected on sea bream aquaculture cages and on a rocky coastal tract located about 1.2 km from the cages, as the control site. Patella caerulea microbiome variations were explained in the broad marine metacommunity context, assessing the water and sediment microbiome composition at both sites, and characterizing the microbiome associated with the farmed sea bream. The P. caerulea digestive gland microbiome at the aquaculture site was characterized by a lower diversity, the loss of microorganisms sensitive to heavy metal contamination, and by the acquisition of fish pathogens and parasites. However, we also observed possible adaptive responses of the P. caerulea digestive gland microbiome at the aquaculture site, including the acquisition of putative bacteria able to deal with metal and sulfide accumulation, highlighting the inherent microbiome potential to drive the host acclimation to stressful conditions.
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